Are you making use of S4 classes? If so see the threads on slowness in R-patched in the last 48 hours: R-devel will be similar to R-patched was the last time a branch update was done.
On Wed, 4 Jun 2003, Jeff Gentry wrote: > I've noticed that some of our Bioconductor code was running drastically > slower under current R-devel vs. current R-patched - one example is below > using a ttest. I have the following snippet of code that demonstrates the > problem while avoiding "real" code that takes an extremely long time to > finish on R-devel: > > library(genefilter) > data(eset) > eset$cov1 > z <- ttest(eset$cov1, p=0.01) > gf <- filterfun(z) > system.time(genefilter(eset, gf)) > > (this requires the genefilter & Biobase packages from Bioconductor) > > Using R-1.7.0p I had the following output: What is that? We do have 1.7.1 beta now. > > data(eset) > > eset$cov1 > [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 > > z <- ttest(eset$cov1, p=0.01) > > gf <- filterfun(z) > > system.time(genefilter(eset, gf)) > [1] 41.73 2.04 44.45 0.00 0.00 > > And using R-devel, I have: > > data(eset) > > eset$cov1 > [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 > > z <- ttest(eset$cov1, p=0.01) > > gf <- filterfun(z) > > system.time(genefilter(eset, gf)) > [1] 80.56 4.20 85.12 0.00 0.00 > > Any ideas what might be causing this? > > Thanks > -Jeff > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
